The COVID-19 pandemic lockdowns were accompanied by an abrupt transition from face-to-face education to online education. The aim of this study was to evaluate the impact of the COVID-19 pandemic on academic functioning and mood in Dutch pharmacy students and PhD candidates. A total of n = 341 participants completed an online survey including questions on mood and academic functioning, assessed retrospectively for before and during the COVID-19 pandemic. Overall, during COVID-19 lockdown, significantly more time was spent on academic activities, and study grades/output significantly improved. However, the overall effects were of small magnitude, and there was great variability among students, reporting either improved, unchanged or poorer academic functioning. Compared to before COVID-19, the lockdown periods were associated with significantly increased levels of stress, anxiety, depression, fatigue, and loneliness, and a significant reduction in optimism and happiness. Significant negative correlations were found between ‘performance quality’ and stress, ‘performance quality’ and fatigue, ‘study grades/output’ and stress, and between ‘study grades/output’ and fatigue. Correlations of mood and items related to academic interactions were not statistically significant. Differential effects were seen when the data was analyzed according to sex, living situation, and ethnicity, revealing that women, students living alone, and those with a migration background reported that COVID-19 lockdowns had greater negative mood effects and a more negative impact on academic functioning. Poorer sleep quality and reduced quality of life were significantly associated with reduced mood, as well as reduced academic performance quality and role satisfaction. Regression analysis revealed that being young and not having a non-Western migration background were predictors of improved performance quality. However, only being young was a significant predictor of improved study grades/output during the COVID-19 pandemic. Increased levels of stress and fatigue were significant predictors of both reduced performance quality and poorer study grades/output during the COVID-19 pandemic. In conclusion, for the sample as a whole, the transition to online education during the COVID-19 lockdown was judged as having significant positive effects on academic performance. The lockdown periods were associated with significantly reduced mood and reduced social interactions. It should be taken into account that about one third of students reported academic functioning to be poorer during the COVID-19 pandemic. This represents a substantial group of students who require more attention and guidance to make a successful transition to online education and cope with lockdown-associated stress and fatigue.